Actually yes. When exporting...
However, even though MathML is part of both the HTML5 and EPUB 3 standards, I don't know of a way to get the MathML out of InDesign and into these other formats. I can feel my way around InDesign, but honestly, I know a lot more about MathML than I do about ID. If someone else knows a way to do this, I'd really like to know.
And to clarify my previous response, I was assuming graphical equations (EPS or PDF) in InDesign. I don't know of a way to get MathML out of that environment. I might expect different results if the document text included MathML markup, but I don't know why someone would follow that workflow.